Friday, February 27, 2009

Databases and Algorithms for Pathway Bioinformatics presented by Peter D. Karp


This talk will provide an overview of the BioCyc collection of 370 Pathway/Genome Databases that is available at URL, and of the Pathway Tools software that underlies BioCyc. The BioCyc collection includes the EcoCyc DB, which describes the metabolic and genetic regulatory network of Escherichia coli, and the MetaCyc DB, which describes 1000+ metabolic pathways that were experimentally elucidated in more than 1200 organisms.

Pathway Tools includes a large biological ontology that facilitates the representation of complex biological knowledge with high fidelity; a set of inference modules for inferring new layers of biological information above an annotated genome, including inferring the metabolic pathway map of an organism, predicting which genes fill missing reactions in the predicted pathways, and predicting the operons of the organism; and visualization tools that support web publishing, querying, and analyses of these data. Pathway databases provide a rich environment for data mining
- Association for Computing Machinery (ACM)

Peter D Karp - Peter D. Karp is director of the Bioinformatics Research Group at SRI International. Dr. Karp is the bioinformatics architect of the EcoCyc and MetaCyc databases. He has developed algorithms for visualization of metabolic pathways, and for prediction of metabolic pathways from genome data. His research interests include metabolic pathway bioinformatics, genome annotation, scientific visualization, biological ontologies, and database interoperation. Dr. Karp has worked in the Artificial Intelligence Center at SRI International since 1991, where he directs the Bioinformatics Research Group. Dr. Karp has authored more than 90 publications in bioinformatics and computer science. He received the Ph.D. degree in Computer Science from Stanford University in 1989.


  1. you have so many videos... it's a pity transcripts aren't available.

  2. I'm sure I could find transcripts for some of these, I just didn't think their was demand since text on the web is so plentiful and videos are rare, but from now on I will always post transcript links if they are available. Thanks for posting the comment :)